Molecular Genetics and Genomics最新文献

Blackcurrant (Ribes nigrum L.), a nutrient-rich cold-climate berry, accumulates ascorbic acid (AsA) and flavonoids critical for fruit quality, yet their regulatory mechanisms during development remain poorly characterized. This study systematically investigated AsA and flavonoid dynamics across four developmental stages (young, expansion, veraison, ripe) in two contrasting varieties, 'Adelinia' and 'Heifeng', while integrating transcriptomics to elucidate metabolic pathways and regulatory networks. We observed a progressive decline in AsA content during fruit maturation, governed by coordinated regulation of biosynthesis (GDP-L-galactose phosphorylase-driven) and recycling pathways (mediated by monodehydroascorbate reductase). Flavonoid levels peaked at the young fruit stage, sharply decreased during veraison, and showed varietal specificity, with 'Heifeng' exhibiting higher accumulation. Co-expression networks identified 4 core structural genes and 6 transcription factors (TFs) regulating AsA metabolism, alongside 8 structural genes and 9 TFs associated with flavonoid biosynthesis. Comparative analysis of fruit size revealed divergent hormone signaling between varieties, with auxin- and cytokinin-related DEGs in the plant hormone transduction pathway (ko04075) strongly correlated with cell expansion. Photosynthesis-antenna protein pathway genes (ko00196) further contributed to size variation, suggesting energy allocation trade-offs during ripening. These findings advance the molecular understanding of AsA and flavonoid regulation in blackcurrant, highlighting cultivar-specific metabolic strategies. The identified genes and TFs provide actionable targets for breeding programs aimed at enhancing nutritional quality and yield, while insights into hormone signaling offer practical frameworks for optimizing growth regulator applications in cultivation.

Soybean seed width (SW) is a pivotal quantitative trait influencing both seed yield and appearance quality, controlled by a complex interplay of multiple genes and environmental factors. This research was undertaken to identify significant genetic loci and candidate genes associated with SW, thereby facilitating the development of molecular markers crucial for advancing soybean breeding programs. In this study, a four-way recombinant inbred line (FW-RIL) population, derived from the cross of (Kenfeng14 × Kenfeng15) × (Heinong48 × Kenfeng19),¹ alongside a diverse germplasm population (GP) comprising 455 soybean cultivars, served as the genetic material. Phenotypic measurements of SW were meticulously recorded for the FW-RILs across three distinct environments and for the GP across four environments. Subsequent linkage analysis in the FW-RIL population and genome-wide association studies (GWAS) in the GP were conducted to map the quantitative trait loci (QTLs) and quantitative trait nucleotides (QTNs) underlying SW. These analyses successfully identified a total of 51 QTLs and 103 QTNs associated with SW. Furthermore, detailed investigation of seven QTNs attenuation regions located within the consistently detected qSW-7-2 region was performed to predict potential candidate genes. This process led to the selection of three promising genes; Glyma.07G004700, Glyma.07G006300, and Glyma.07G013700 based on the integrated evidence from sequence variation analysis among parental lines, comprehensive haplotype analysis within the mapping populations, and relevant functional annotation. The comprehensive identification of these QTLs, QTNs, and particularly the three prioritized candidate genes, offers significant insights into the genetic control of soybean seed width and provides a robust foundation for the development of effective molecular markers to enhance the efficiency of marker-assisted selection for improved soybean yield.

High mobility group (HMG) proteins, the second most abundant chromatin proteins after histones, play essential roles in eukaryotic gene regulation. Among these, High Mobility Group Box 3 (HMGB3) is critical for DNA repair and has gained prominence in cancer biology due to its involvement in tumorigenesis and cancer progression. This study explores the cellular and molecular mechanisms underlying HMGB3's oncogenic functions, with a focus on its potential as a prognostic biomarker and therapeutic target. We highlight that HMGB3 is frequently overexpressed in tumor tissues and discuss its association with poor clinical outcomes. Furthermore, we examine the ceRNA network and other regulatory pathways influencing HMGB3 expression, emphasizing their implications for RNA-based therapies. By comprehensively reviewing HMGB3's role across multiple cancer types, this work provides insights into novel strategies for targeting HMGB3 to improve cancer treatment efficacy. Our findings underscore the therapeutic potential of modulating HMGB3 expression and pave the way for future research into precision oncology approaches.

Inhibition of the activity of Pma1, a widely conserved P-type proton exporting ATPase, has been shown to extend the chronological lifespan (CLS) in fission yeast Schizosaccharomyces pombe. To develop a specific inhibitor for Pma1 of S. pombe, we focused on Si01, a candidate inhibitor of Saccharomyces cerevisiae Pma1. First, we have established a method for synthesis of Si01 and then investigated its Pma1 inhibitory activity and lifespan extension effect in fission yeast. Second, we also synthesized derivatives of Si01 and determined the minimum structure required for inhibition of S. pombe Pma1. Here we showed that the inhibitory activity of Pma1 correlates with the effect of lifespan extension. Si01 reduced the activity of purified Pma1 protein and extended the CLS of not only fission yeast but also budding yeast. These results provide a molecular basis for understanding the mechanism of Pma1 inhibition and the potential for developing molecules that regulate lifespan.

Myogenesis, a multistep process involving myoblast proliferation and differentiation, is critical for determining the economic value of beef cattle. While long noncoding RNAs (lncRNAs) are known to regulate myoblast proliferation, their specific mechanisms remain unclear. This study investigates the role of lncBNIP3 in bovine myoblast proliferation and examines the effects of its knockdown on cellular biological characteristics. Using quantitative real-time PCR (qRT-PCR), lncBNIP3 expression was observed to be higher in muscle tissues compared to other tissues in both 1-day-old and 24-month-old Qinchuan cattle. Knockdown of lncBNIP3 expression upregulated the mRNA levels of proliferation-related genes, as confirmed by qRT-PCR, and subsequently enhanced cellular proliferation, as demonstrated through EdU assays, flow cytometry, and CCK-8 analysis. Transcriptomic sequencing of myoblasts revealed that differentially expressed genes (DEGs) were significantly enriched in pathways associated with DNA replication and the cell cycle. Shared DEGs were primarily enriched in the minichromosome maintenance (MCM) gene family. Additionally, qRT-PCR and transcriptomic sequencing results revealed that the knockdown of lncBNIP3 expression significantly upregulated the mRNA levels of MCM family genes, including MCM2 and MCM3. Fluorescence activity assays further showed that lncBNIP3 knockdown significantly enhanced the promoter activities of MCM2 and MCM3. These findings suggest that interference with lncBNIP3 expression promotes the proliferation of bovine myoblasts, potentially through transcriptional regulation of the MCM gene family. This study provides novel insights into the regulatory functions of lncRNAs in muscle development.

This paper identifies gene candidates differentially expressed in the porcine brain during sepsis, designed for eventual application in human clinical care for earlier detection of sepsis, as no known biomarkers currently exist. Sepsis associated encephalopathy (SAE) is characterized by dysregulated molecular pathways of the immune response impinging upon normal central nervous system (CNS) function and ultimately resulting in lasting cognitive and behavioral impairments. This study seeks to identify gene candidates that exhibit altered transcriptional expression during sepsis. Twelve Yorkshire pigs (n = 6 for saline control and lipopolysaccharide group) were utilized. LPS injection rate was 0.5-0.75 mL/kg resulting in death within 5-10 h. Brain tissue was collected and analyzed via bulk RNA-seq, and corresponding computational genomic analysis. Multiple genes demonstrated significant differential expression in the early septic brain, correlating with endothelial cell disruption, immune/inflammatory alterations, and potential alterations in microglia. Gene candidates downregulated include: OCLN, SLC19A3, and SLC52A3. Genes upregulated include: ICAM1, IRF1, CXCL10, and ZFP36. Specific gene candidates were identified as early changes in the septic brain that could be targets to prevent long-term cognitive and behavioral changes seen in sepsis survivors and establish a baseline diagnostic panel to interrogate in animal models with the goal of advancing treatments for human patients who experience sepsis.

India's northeastern region, particularly Meghalaya, a melting pot of diverse ethnic and racial groups that have been shaped by ancient migrations and the natural barriers posed by the Himalayas. The Hajong tribe, who live mainly in the Garo Hills of Meghalaya, reflect this diversity, sharing cultural similarities with the Tibetan and Bhutanese populations. Historically regarded as immigrants to Arunachal Pradesh, the Hajongs' genetic relationship with the greater Himalayan region makes them an ideal subject for estimation of genetic attributes. This study analyzed 23 autosomal STR markers to assess the genetic diversity of Hajong tribe with emphasis on forensic parameters. Among the 23 autosomal STR markers analyzed, several loci including SE33, FGA, and D18S51 exhibited high polymorphic information content and paternity index values, reflecting their strong forensic utility in the Hajong population. The combined Power of Exclusion (PE) and Power of Discrimination (PD) was 0.999999999 and 0.999999999, respectively, whereas the Total Paternity Index (TPI) and the Combined Matching Probability (PM) was 756014064.7 and 1.3214E-27. The fixation index, F = - 0.016 ± 0.014, showed very minimal intra-population differentiation. Genetic relationship assessment, including NJ dendrograms and MDS plots, revealed a close genetic affinity between Hajong and populations from Tibet, Bhutan, Nepal, and Myanmar, reflecting a shared ancestral relationship. STRUCTURE analysis revealed well-defined clustering, with limited admixture in the Hajong population, indicating genetic distinctiveness. This study reflects the genetic individuality of the Hajong tribe and its utility for forensic studies in kinship analysis. Such studies will, further, help in analyzing population dynamics in Northeast India by tracing the history of migration and interrelationships among Himalayan populations.

Salt stress adversely impacts crop growth and development, resulting in stunted growth and diminished grain yield. Therefore, this study explores the synergetic effects of seed priming with iron nanoparticles (FeNPs) integrated with a genome-wide association study (GWAS) on the phenotypic, biochemical, and agronomic traits of 138 barley accessions under control, salinity stress, and seed iron priming treatments. A normal phenotypic distribution was observed across all accessions under the tested conditions, with significant natural phenotypic variation in response to the treatments. Remarkably, seed priming with FeNPs showed a significant enhancement in superoxide dismutase (SOD) activity and selective modulation of catalase (CAT) and glutathione reductase (GR) activities, indicating a targeted oxidative stress response. Compared to control and salinity stress conditions, priming with FeNPs showed substantial increases in all agronomic traits, including spike length (SL), number of spikelets per spike (NSS), number of grains per spike (NGS), weight of grains per spike (WGS), and thousand kernel weight (TKW), suggesting its potential to mitigate the adverse effects of salinity and promote better crop performance. Based on GWAS analysis, sixteen highly significant marker associations/candidate genes were detected to be associated with antioxidant components. Using quantitative real-time PCR analysis (RT-qPCR), FeNPs seed priming effectively modulates the plant's transcriptional response to salinity stress by balancing rapid gene activation with sustained stress adaptation. This approach mitigates excessive defense responses while promoting long-term stability through controlled upregulation of key genes, such as PP2C, Phosphotransferase, Terpene Synthase Putative, and RWP-RK. The findings support the potential of FeNPs as a biotechnological tool to enhance crop resilience and optimize agronomic performance under adverse environmental conditions.

Nitrogen (N) induced environmental pollution from rice cultivation has resulted in undesired environmental impacts. To minimize the impacts, improvement of inherent NUE is very crucial in rice as it has the lowest NUE among the cereals. Though many family based and association based QTL studies have been reported earlier on NUE in rice, the reports on indica rice and precise evaluation of root parameters till physiological maturity is lacking. This study reports the identification of candidate genes and QTLs through a genome-wide association study (GWAS) involving 96 diverse indica rice genotypes, grown under contrasting N regimes in hydroponics till maturity. Genotyping was carried out using 80 K Affymetrix chip containing 47,686 curated SNP markers. The differential response of ten different N-responsive traits indicated separate breeding program for each N-regime. The population structure analysis revealed two sub-populations with varying degrees of admixtures in the association panel. The linkage disequilibrium (LD) analysis revealed a LD block of 108.4 kb. GWAS using MLM, FarmCPU, and BLINK could identify 568 marker-trait associations (MTAs) across different traits and N-conditions. Out of 24 common MTAs identified, 13 were novel with 156 candidate genes in the genomic region spanning the LD blocks. Yield and root-related MTAs were found to be the most prominent. N-responsive genes were found to be associated with other abiotic stresses like drought and salinity, as seen from the available literature. Candidate genes (OsWAK15, OsNIN8, OsHCT2, Os02 g0612900, Os02 g0613100, and Os02 g0612700) showed a similar expression pattern under N-stress in both N use- efficient and inefficient genotypes, which can be potential targets for modulating gene expression for N stress tolerance. These MTAs and candidate genes can serve as key resources for enhancement of NUE in rice upon functional validation.

The objective of this study was to characterize the virulence characteristics of a collection of Klebsiella pneumoniae isolates collected from different clinical sources. A collection of 60 non-repetitive K. pneumoniae isolates, was studied. In vitro, virulence was analyzed by testing the survival of bacteria in pooled human serum. Isolates were typed by MLST. The genomes of 23 K. pneumoniae isolates, representatives of different STs and virulence profiles, were completely sequenced using the Illumina platform. Of note, 26/60 of K. pneumoniae isolates were resistant to killing by complement. Serum-resistant isolates belonged to distinct STs. Analysis of WGS data with VFDB showed the presence of several virulence genes related various virulence functions. Specifically, serum-resistant isolates carried a higher number of ORFs, which were associated with serum resistance, compared to serum-sensitive isolates. Additionally, analysis of WGS data showed the presence of multiple plasmid replicons that could be involved with the spread and acquisition of resistance and virulence genes. In conclusion, analysis of virulence characteristics showed that an important percentage (31.6%) of K. pneumoniae isolates were in vitro virulent by exhibiting resistance to serum. Thus, the presence of several virulence factors, in combination with the presence of multidrug resistance, could challenge antimicrobial therapy of infections caused by such bacteria.